Remove duplicates and then convert them with ggplotly.
p <-
ggplot(mtcars, aes(vs, am)) +
geom_point(alpha = 0.1)
plotly::ggplotly(p)
p <-
ggplot(mtcars, aes(vs, am)) +
geom_point(alpha = 0.1, stat = "unique")
plotly::ggplotly(p)